MolNFT v1 · #164119 · protein
Structure of coxsackievirus A10 complexed with its receptor KREMEN1
6SNW · Capsid protein VP1: “Structure of coxsackievirus A10 complexed with its receptor KREMEN1”. Electron microscopy, 2 ligands (SPH, NAG), 13 pockets (best druggability 0.80). MolNFT v1 #164119 on GenesisL1: 3D structure, binding sites…
- PDB
- 6SNW
- Type
- protein
- Length
- 1,114 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1; Coxsackievirus VP2; Capsid protein VP3; Coxsackievirus VP4; Kremen…
- EC
- 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48
- UniProt
- Q6JKR9, Q96MU8
- Ligands
- SPH, NAG
- Pockets
- 13 · best druggability 0.80
Structure
electron microscopy · 5 distinct chains · 9% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 293 | 12% helix, 26% strand | Q6JKR9 |
| B | Coxsackievirus VP2 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 246 | 9% helix, 31% strand | Q6JKR9 |
| C | Capsid protein VP3 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 240 | 10% helix, 31% strand | Q6JKR9 |
| D | Coxsackievirus VP4 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 41 | 7% helix, 2% strand | Q6JKR9 |
| E | Kremen protein 1 | protein | 294 | 4% helix, 26% strand | Q96MU8 |
Ligands and binding sites
- SPH · Sphingosine · ligand · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 951 | 0.80 | 0.82 | 111 | SPH |
| 2 | 100 | 0.74 | 0.95 | 24 | empty |
| 3 | 174 | 0.53 | 0.79 | 35 | empty |
| 4 | 212 | 0.51 | 0.76 | 28 | empty |
| 5 | 166 | 0.51 | 0.78 | 30 | empty |
Interfaces
9 interfaces between chains.
- A–C · 3923 Ų buried · 64 hydrogen bonds · protein-protein
- A–B · 2501 Ų buried · 43 hydrogen bonds · protein-protein
- B–C · 1754 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 1198 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 901 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q6JKR9
- Every structure of UniProt Q96MU8
- Elsewhere: RCSB PDB 6SNW · PDBe 6SNW · UniProt Q6JKR9 · UniProt Q96MU8
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